rformassspectrometry
feature request: set values below a threshold as NA
The normalization function in SCeptre (from Schoof et al. 2021 paper) performs at some moment an NA thresholding, that is quantitative values below a given threshold are set as NA. I personally think this should not be performed in a normalization function, but it could be implemented in a separate function. This would be very similar to zeroIsNA but it must require an additional argument that provides the threshold below which the data is considered missing.
Do you think this functionality is worth being included in QFeatures? Or do we already have this but I missed it?
I don't think we should change zeroIsNA(x) to zeroIsNA(x, ..., threshold = 0), but we could have a function setToZero(x, min) that sets values <= min to 0. Or could you not simply create that function and apply it on the fly (as a example of how to process assays with user-provided functions) ?
